Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image ( https://drive.google.com/file/d/11GJntUJU7-phc-Bz-hWBICvQWFIGUJDI/view?usp=sharing ).
Another question is that when I try to increase the deform rate, there is a warning: triclinic box is to skewed ... cannot fix pbc. And the simulation will stop after 1000 steps. How to prevent this? I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia.
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